fixed/improved integration tests

[petraglyph]

Fixed the extract_all_files test not properly recursing into sub-directories.

Added a file tree (under include_dir/tests/tree) explicitly for integration testing.

• This tree is deeper than the source code previously used (2 layers of directories, instead of only 1) which allows more thorough testing, and reveals the bug in the extract_all_files test.
• This also keep the tests working when built from the crate source (which will locate target/ in the crate root, previously causing changes in tests directory contents between building to testing)